My pick for the cutest Pokémon is Amaura. It is a nice blue colored Pokémon with big eyes and an expressive sail that changes color with its emotions. Also the Diamond on its body is a nice touch.
I love Chikorita for so, so many reasons. Plant Dino! The fact that it typically ranks so low as one of the least-loved starters makes me love it more.
Barring that, Rowlett, my soft baby owl.